NPASS Compound

Natural Product: NPC476407

Natural Product ID	NPC476407
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Platyphyllonol-5-Xylopyranoside
IUPAC Name	(5S)-7-(3-hydroxyphenyl)-1-(4-hydroxyphenyl)-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyheptan-3-one
Synonyms	Platyphyllonol-5-Xylopyranoside
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL596919
PubChem CID	46230810
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 62 64 0 0 0 0 0 0 0 0999 V2000 -2.2765 -2.3225 -2.7183 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3107 -3.6867 -2.0491 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5484 -3.6448 -0.7303 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1351 -2.4771 0.0618 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8295 -1.2281 -0.7240 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6778 -1.3197 -1.8686 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1520 -0.0411 -0.1535 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1370 0.9006 -0.0621 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3424 1.9961 -1.1014 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2455 3.0240 -1.0070 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3926 4.0609 -2.0730 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2203 3.8634 -3.2818 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1144 4.8030 -4.3142 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6239 5.9456 -4.0979 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2418 6.1574 -2.8952 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1191 5.2035 -1.8843 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7618 4.5324 -5.5061 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8325 1.4404 1.2693 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4299 0.4434 2.2849 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2476 0.0127 3.0569 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9554 -0.0582 2.3962 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0844 -1.1182 3.4755 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4851 -1.6109 3.5663 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3528 -1.0041 4.4221 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6566 -1.4852 4.4631 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0132 -2.5398 3.6489 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1343 -3.1391 2.7962 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8351 -2.6658 2.7501 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3176 -3.0089 3.7006 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6603 -2.4752 1.3599 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6817 -4.8573 -0.1134 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5933 -4.1438 -1.8554 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2281 -2.1121 -3.0456 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9367 -2.3453 -3.5845 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7862 -4.3901 -2.7248 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4876 -3.4836 -1.0005 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2244 -2.6460 0.0857 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7679 -1.3010 -1.0479 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2200 0.3638 -0.4649 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3661 1.5694 -2.1237 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2903 2.5197 -0.8450 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3071 3.5803 -0.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7715 2.6195 -1.0557 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7972 2.9839 -3.4684 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7140 6.6807 -4.8865 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8217 7.0457 -2.7080 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6084 5.3822 -0.9464 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4000 4.8800 -6.3802 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0434 2.1649 1.2096 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6761 2.0865 1.6122 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6396 0.7865 2.6770 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3485 -0.4246 1.4261 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7954 -0.6386 4.4328 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3602 -1.9444 3.2871 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0851 -0.1720 5.0696 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3950 -1.0657 5.1053 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3977 -3.9633 2.1523 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1038 -3.1008 2.0984 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9351 -2.8889 2.9157 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2241 -2.9829 1.9682 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5816 -5.1807 0.0342 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2854 -3.5802 -2.2674 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 5 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 13 17 1 0 8 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 26 29 1 0 4 30 1 0 3 31 1 0 2 32 1 0 6 1 1 0 16 11 1 0 28 23 1 0 1 33 1 0 1 34 1 0 2 35 1 0 3 36 1 0 4 37 1 0 5 38 1 0 8 39 1 0 9 40 1 0 9 41 1 0 10 42 1 0 10 43 1 0 12 44 1 0 14 45 1 0 15 46 1 0 16 47 1 0 17 48 1 0 18 49 1 0 18 50 1 0 21 51 1 0 21 52 1 0 22 53 1 0 22 54 1 0 24 55 1 0 25 56 1 0 27 57 1 0 28 58 1 0 29 59 1 0 30 60 1 0 31 61 1 0 32 62 1 0 M END

Standard InCHIKey	FITQTWOHVZNKOP-QOXFPCGXSA-N
Standard InCHI	InChI=1S/C24H30O8/c25-17-8-4-15(5-9-17)6-10-19(27)13-20(11-7-16-2-1-3-18(26)12-16)32-24-23(30)22(29)21(28)14-31-24/h1-5,8-9,12,20-26,28-30H,6-7,10-11,13-14H2/t20-,21+,22-,23+,24-/m0/s1
SMILES	C1C(C(C(C(O1)OC(CCC2=CC(=CC=C2)O)CC(=O)CCC3=CC=C(C=C3)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	446.19	Volume:	449.857 ? Van der Waals volume.
Dense:	0.992	LogP:	1.012 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.482 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.75 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	19.0
TPSA:	136.68 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	5.0	Rings:	3.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.37	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.886	Fsp³:	0.458
MCE-18:	62.429 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.045	Fluc inhibitor:	0.036 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.021 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.304 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.176	Promiscuous compounds:	0.151

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.984	MDCK Permeability:	-4.984
Pgp-inhibitor:	0.131	Pgp-substrate:	0.736
PAMPA:	0.963 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.404	30% Bioavailability (F30%):	0.979
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.02
Plasma Protein Binding (PPB):	79.129%	Volume Distribution (VD):	-0.277
Fu:	21.069% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.359
OATP1B3 inhibitor:	0.931	BCRP inhibitor:	0.093
BSEP inhibitor:	0.996

ADMET: Metabolism

CYP1A2-inhibitor:	0.083	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.994	CYP2C19-substrate:	0.006
CYP2C9-inhibitor:	0.669	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.01	CYP2D6-substrate:	0.998
CYP3A4-inhibitor:	0.003	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.957 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

3.281

Half-life (T1/2):

1.644

ADMET: Toxicity

hERG Blockers:	0.295	hERG Blockers (10um):	0.777
Human Hepatotoxicity (H-HT):	0.53	Drug-induced Liver Injury (DILI):	0.039
AMES Toxicity:	0.379	Rat Oral Acute Toxicity:	0.089
Maximum Recommended Daily Dose:	0.54	Skin Sensitization:	0.345
Carcinogencity:	0.088	Eye Corrosion:	0.0
Eye Irritation:	0.361	Respiratory Toxicity:	0.05
Drug-induced Neurotoxicity:	0.55	Ototoxicity:	0.928
Hematotoxicity:	0.052	Drug-induced Nephrotoxicity:	0.44
Genotoxicity:	0.101	RPMI-8226 Immunitoxicity:	0.033
A549 Cytotoxicity:	0.106	Hek293 Cytotoxicity:	0.827
BCF:	0.842 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.627 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.168 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.433 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	bark	n.a.	n.a.	PMID[20045319]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26341132]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
EC50	1
Ratio	1

Activity Type	# Activity
Organism	1
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT742	Organism	Influenza A virus	Influenza A virus	EC50	=	56100.0	nM	PMID[24456578]
NPT2	Others	Unspecified	n.a.	Ratio	>	10.0	n.a.	PMID[21334896]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC476407 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	11614
0.1-0.2	33425
0.2-0.3	4449
0.3-0.4	305
0.4-0.5	49
0.5-0.6	4
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	4
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8833	High Similarity	NPC180171
0.875	High Similarity	NPC158673
0.85	High Similarity	NPC158325
0.85	High Similarity	NPC193018
0.7833	Intermediate Similarity	NPC103398
0.7833	Intermediate Similarity	NPC608691
0.6562	Remote Similarity	NPC17968
0.6562	Remote Similarity	NPC469705
0.6522	Remote Similarity	NPC471066
0.6286	Remote Similarity	NPC471095
0.6027	Remote Similarity	NPC164172
0.5882	Remote Similarity	NPC94179
0.5882	Remote Similarity	NPC293686
0.5316	Remote Similarity	NPC28776
0.5063	Remote Similarity	NPC469696

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC476407 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3358
0.1-0.2	5479
0.2-0.3	312
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data